Job ID = 14520623 SRX = SRX11781089 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:27:32 prefetch.2.10.7: 1) Downloading 'SRR15481032'... 2022-01-15T10:27:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:29:04 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:29:04 prefetch.2.10.7: 1) 'SRR15481032' was downloaded successfully 2022-01-15T10:29:04 prefetch.2.10.7: 'SRR15481032' has 0 unresolved dependencies Read 15808665 spots for SRR15481032/SRR15481032.sra Written 15808665 spots for SRR15481032/SRR15481032.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:02 15808665 reads; of these: 15808665 (100.00%) were paired; of these: 3375710 (21.35%) aligned concordantly 0 times 11265335 (71.26%) aligned concordantly exactly 1 time 1167620 (7.39%) aligned concordantly >1 times ---- 3375710 pairs aligned concordantly 0 times; of these: 166214 (4.92%) aligned discordantly 1 time ---- 3209496 pairs aligned 0 times concordantly or discordantly; of these: 6418992 mates make up the pairs; of these: 4458480 (69.46%) aligned 0 times 1713278 (26.69%) aligned exactly 1 time 247234 (3.85%) aligned >1 times 85.90% overall alignment rate Time searching: 00:17:03 Overall time: 00:17:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 4356544 / 12597994 = 0.3458 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:00:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:21: 1000000 INFO @ Sat, 15 Jan 2022 20:00:28: 2000000 INFO @ Sat, 15 Jan 2022 20:00:36: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:00:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:43: 4000000 INFO @ Sat, 15 Jan 2022 20:00:50: 5000000 INFO @ Sat, 15 Jan 2022 20:00:51: 1000000 INFO @ Sat, 15 Jan 2022 20:00:58: 6000000 INFO @ Sat, 15 Jan 2022 20:00:59: 2000000 INFO @ Sat, 15 Jan 2022 20:01:05: 7000000 INFO @ Sat, 15 Jan 2022 20:01:07: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 20:01:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:01:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:01:13: 8000000 INFO @ Sat, 15 Jan 2022 20:01:15: 4000000 INFO @ Sat, 15 Jan 2022 20:01:21: 9000000 INFO @ Sat, 15 Jan 2022 20:01:22: 1000000 INFO @ Sat, 15 Jan 2022 20:01:23: 5000000 INFO @ Sat, 15 Jan 2022 20:01:30: 10000000 INFO @ Sat, 15 Jan 2022 20:01:31: 6000000 INFO @ Sat, 15 Jan 2022 20:01:31: 2000000 INFO @ Sat, 15 Jan 2022 20:01:38: 11000000 INFO @ Sat, 15 Jan 2022 20:01:38: 7000000 INFO @ Sat, 15 Jan 2022 20:01:40: 3000000 INFO @ Sat, 15 Jan 2022 20:01:46: 12000000 INFO @ Sat, 15 Jan 2022 20:01:47: 8000000 INFO @ Sat, 15 Jan 2022 20:01:49: 4000000 INFO @ Sat, 15 Jan 2022 20:01:54: 13000000 INFO @ Sat, 15 Jan 2022 20:01:55: 9000000 INFO @ Sat, 15 Jan 2022 20:01:57: 5000000 INFO @ Sat, 15 Jan 2022 20:02:02: 14000000 INFO @ Sat, 15 Jan 2022 20:02:04: 10000000 INFO @ Sat, 15 Jan 2022 20:02:06: 6000000 INFO @ Sat, 15 Jan 2022 20:02:10: 15000000 INFO @ Sat, 15 Jan 2022 20:02:13: 11000000 INFO @ Sat, 15 Jan 2022 20:02:14: 7000000 INFO @ Sat, 15 Jan 2022 20:02:18: 16000000 INFO @ Sat, 15 Jan 2022 20:02:21: 12000000 INFO @ Sat, 15 Jan 2022 20:02:23: 8000000 INFO @ Sat, 15 Jan 2022 20:02:26: 17000000 INFO @ Sat, 15 Jan 2022 20:02:30: 13000000 INFO @ Sat, 15 Jan 2022 20:02:31: 9000000 INFO @ Sat, 15 Jan 2022 20:02:35: 18000000 INFO @ Sat, 15 Jan 2022 20:02:37: 14000000 INFO @ Sat, 15 Jan 2022 20:02:38: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:02:38: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:02:38: #1 total tags in treatment: 8107602 INFO @ Sat, 15 Jan 2022 20:02:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:02:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:02:39: #1 tags after filtering in treatment: 4637616 INFO @ Sat, 15 Jan 2022 20:02:39: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:02:39: #1 finished! INFO @ Sat, 15 Jan 2022 20:02:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:02:39: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 20:02:39: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 20:02:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:02:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:02:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:02:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:02:39: #2 predicted fragment length is 70 bps INFO @ Sat, 15 Jan 2022 20:02:39: #2 alternative fragment length(s) may be 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 bps INFO @ Sat, 15 Jan 2022 20:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05_model.r WARNING @ Sat, 15 Jan 2022 20:02:39: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:02:39: #2 You may need to consider one of the other alternative d(s): 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 WARNING @ Sat, 15 Jan 2022 20:02:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:02:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:02:40: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:02:45: 15000000 INFO @ Sat, 15 Jan 2022 20:02:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.05_summits.bed INFO @ Sat, 15 Jan 2022 20:02:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:02:49: 11000000 INFO @ Sat, 15 Jan 2022 20:02:53: 16000000 INFO @ Sat, 15 Jan 2022 20:02:57: 12000000 INFO @ Sat, 15 Jan 2022 20:03:02: 17000000 INFO @ Sat, 15 Jan 2022 20:03:05: 13000000 INFO @ Sat, 15 Jan 2022 20:03:10: 18000000 INFO @ Sat, 15 Jan 2022 20:03:13: 14000000 INFO @ Sat, 15 Jan 2022 20:03:14: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:03:14: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:03:14: #1 total tags in treatment: 8107602 INFO @ Sat, 15 Jan 2022 20:03:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:03:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:03:14: #1 tags after filtering in treatment: 4637616 INFO @ Sat, 15 Jan 2022 20:03:14: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:03:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:03:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:03:14: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 20:03:14: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 20:03:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:03:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:03:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:03:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:03:14: #2 predicted fragment length is 70 bps INFO @ Sat, 15 Jan 2022 20:03:14: #2 alternative fragment length(s) may be 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 bps INFO @ Sat, 15 Jan 2022 20:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10_model.r WARNING @ Sat, 15 Jan 2022 20:03:14: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:03:14: #2 You may need to consider one of the other alternative d(s): 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 WARNING @ Sat, 15 Jan 2022 20:03:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:03:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:03:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:03:20: 15000000 INFO @ Sat, 15 Jan 2022 20:03:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.10_summits.bed INFO @ Sat, 15 Jan 2022 20:03:23: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:03:27: 16000000 INFO @ Sat, 15 Jan 2022 20:03:35: 17000000 INFO @ Sat, 15 Jan 2022 20:03:42: 18000000 INFO @ Sat, 15 Jan 2022 20:03:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:03:45: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:03:45: #1 total tags in treatment: 8107602 INFO @ Sat, 15 Jan 2022 20:03:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:03:45: #1 tags after filtering in treatment: 4637616 INFO @ Sat, 15 Jan 2022 20:03:45: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:03:45: #1 finished! INFO @ Sat, 15 Jan 2022 20:03:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:03:46: #2 number of paired peaks: 130 WARNING @ Sat, 15 Jan 2022 20:03:46: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 15 Jan 2022 20:03:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:03:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:03:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:03:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:03:46: #2 predicted fragment length is 70 bps INFO @ Sat, 15 Jan 2022 20:03:46: #2 alternative fragment length(s) may be 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 bps INFO @ Sat, 15 Jan 2022 20:03:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20_model.r WARNING @ Sat, 15 Jan 2022 20:03:46: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:03:46: #2 You may need to consider one of the other alternative d(s): 22,55,70,112,130,168,200,229,269,288,319,334,356,362,402,419,442,467,493,509,582 WARNING @ Sat, 15 Jan 2022 20:03:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:03:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:03:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781089/SRX11781089.20_summits.bed INFO @ Sat, 15 Jan 2022 20:03:55: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 9 millis CompletedMACS2peakCalling